# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Wed May  6 20:31:40 2020
#   Inital geometry file: a 153 line input string
#   Ligand name: 2-[6-[[5-chloranyl-2-[(3~{S},5~{R})-3,5-dimethylpiperidin-1-yl]pyrimidin-4-yl]amino]-1-methyl-2-oxidanylidene-quinolin-3-yl]oxy-~{N}-methyl-ethanamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: CNC(=O)COC1=Cc2cc(Nc3nc(ncc3Cl)N4C[C@@H](C)C[C@@H](C)C4)ccc2N(C)C1=O
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 U52  U52  2-[6-[[5-chloranyl-2-[(3~{S},5~{R})-3,5-dimethylpiperidin-1-yl]pyrimidin-4-yl]amino]-1-methyl-2-oxidanylidene-quinolin-3-yl]oxy-~{N}-methyl-ethanamide  ligand  63  34  .  2021-08-24  2021-08-24  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_U52
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 U52  C4   C   C     0   0.514  -5.3379  -1.9840  -0.2838
 U52  C5   C   CH2   0  -0.310  -4.0431  -1.1890  -0.3342
 U52  C10  C   CR6   0   0.499  -3.7601   2.3095   0.6085
 U52  C13  C   CR16  0  -0.336   0.8374   3.7817   0.2604
 U52  C15  C   CR66  0   0.351  -1.4461   3.0338   0.4436
 U52  C17  C   CR16  0  -0.383   0.3086   1.5048  -0.2495
 U52  C22  C   CR6   0   0.625   3.3699   1.2342  -0.2779
 U52  C24  C   CR6   0   0.641   3.6189  -0.8995   0.5128
 U52  C26  C   CR16  0   0.014   5.3964   0.0284  -0.5292
 U52  C28  C   CH2   0  -0.291   3.6862  -3.2451   1.2274
 U52  N2   N   NH1   0  -0.625  -5.3508  -3.0525  -1.0861
 U52  O3   O   O     0  -0.481  -6.2535  -1.6839   0.4626
 U52  O6   O   O2    0  -0.438  -4.3338   0.1205   0.0789
 U52  O7   O   O     0  -0.476  -4.9364   2.5319   0.8496
 U52  N9   N   NR6   0  -0.601  -2.7841   3.2654   0.7279
 U52  C11  C   CR6   0   0.214  -3.3122   0.9788   0.1675
 U52  C12  C   CR16  0  -0.326  -2.0174   0.7220  -0.0989
 U52  C14  C   CR16  0  -0.319  -0.4867   4.0453   0.5411
 U52  C16  C   CR66  0   0.099  -1.0355   1.7554   0.0384
 U52  C18  C   CR6   0   0.363   1.2556   2.5077  -0.1370
 U52  N19  N   NH1   0  -0.776   2.6059   2.3358  -0.4631
 U52  N20  N   NT    0  -0.491   3.0781  -1.9291   1.2016
 U52  N23  N   N     0  -0.524   2.8585   0.1847   0.3367
 U52  N25  N   N     0  -0.496   4.8800  -1.0273   0.0802
 U52  C27  C   CR6   0  -0.262   4.7043   1.1981  -0.7334
 U52  C29  C   CH1   0  -0.245   2.9470  -4.2032   0.2928
 U52  C30  C   CH2   0  -0.399   1.4565  -4.2129   0.6291
 U52  C31  C   CH1   0  -0.249   0.8439  -2.8148   0.7025
 U52  C32  C   CH2   0  -0.291   1.6900  -1.9320   1.6168
 U52  C33  C   CH3   0  -0.658   3.5476  -5.5993   0.3784
 U52  C34  C   CH3   0  -0.663  -0.5956  -2.8636   1.1937
 U52  H1   H   HCH2  0   0.262  -3.3223  -1.6656   0.3432
 U52  H2   H   HCH2  0   0.263  -3.6066  -1.2018  -1.3393
 U52  H3   H   HCH3  0   0.286  -4.2379   4.6013   1.3921
 U52  H4   H   HCH3  0   0.261  -2.6313   4.8738   2.0675
 U52  H5   H   HCH3  0   0.261  -2.9818   5.3306   0.3896
 U52  H6   H   HCR6  0   0.277   1.5623   4.5809   0.3518
 U52  H7   H   HCR6  0   0.271   0.5909   0.5131  -0.5704
 U52  H8   H   HCR6  0   0.282   6.4201  -0.0593  -0.8784
 U52  H9   H   HCH2  0   0.266   4.7362  -3.1681   0.9585
 U52  H10  H   HCH2  0   0.229   3.6340  -3.6238   2.2550
 U52  H11  H   HCH3  0   0.241  -7.3688  -3.5323  -1.4595
 U52  H12  H   HCH3  0   0.254  -6.1891  -4.8066  -1.7752
 U52  H13  H   HCH3  0   0.242  -6.6304  -4.4098  -0.1132
 U52  H14  H   HNH1  0   0.410  -4.5749  -3.2163  -1.7062
 U52  H15  H   HCR6  0   0.288  -1.6828  -0.2526  -0.4311
 U52  H16  H   HCR6  0   0.291  -0.7547   5.0479   0.8392
 U52  H17  H   HNH1  0   0.405   3.0811   3.1608  -0.7949
 U52  H18  H   HCH1  0   0.222   3.0748  -3.8302  -0.7308
 U52  H19  H   HCH2  0   0.233   0.9129  -4.8220  -0.0993
 U52  H20  H   HCH2  0   0.205   1.3191  -4.7018   1.6027
 U52  H21  H   HCH1  0   0.224   0.8588  -2.3673  -0.2990
 U52  H22  H   HCH2  0   0.232   1.6468  -2.3237   2.6402
 U52  H23  H   HCH2  0   0.268   1.3114  -0.9131   1.6389
 U52  H24  H   HCH3  0   0.217   3.4607  -6.0001   1.3910
 U52  H25  H   HCH3  0   0.231   3.0380  -6.2900  -0.2951
 U52  H26  H   HCH3  0   0.229   4.6057  -5.5965   0.1108
 U52  H27  H   HCH3  0   0.224  -0.6581  -3.3286   2.1801
 U52  H28  H   HCH3  0   0.219  -1.0209  -1.8616   1.2807
 U52  H29  H   HCH3  0   0.232  -1.2264  -3.4394   0.5146
 U52  C8   C   CH3   0  -0.566  -3.1786   4.5948   1.1685
 U52  C1   C   CH3   0  -0.513  -6.4471  -3.9933  -1.1036
 U52  CL1  CL  CL    0  -0.127   5.4320   2.5457  -1.5368

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 U52  C8   N9   single    1.455  0.020  1.455
 U52  O7   C10  double    1.221  0.020  1.221
 U52  N9   C10  single    1.371  0.020  1.371
 U52  N9   C15  single    1.387  0.020  1.387
 U52  C10  C11  single    1.472  0.020  1.472
 U52  C14  C15  aromatic  1.398  0.020  1.398
 U52  C14  C13  aromatic  1.379  0.020  1.379
 U52  C33  C29  single    1.522  0.020  1.522
 U52  C15  C16  aromatic  1.403  0.020  1.403
 U52  C11  O6   single    1.337  0.020  1.337
 U52  C11  C12  double    1.347  0.020  1.347
 U52  O3   C4   double    1.219  0.020  1.219
 U52  O6   C5   single    1.404  0.020  1.404
 U52  C13  C18  aromatic  1.399  0.020  1.399
 U52  C16  C12  single    1.432  0.020  1.432
 U52  C16  C17  aromatic  1.397  0.020  1.397
 U52  C29  C28  single    1.529  0.020  1.529
 U52  C29  C30  single    1.528  0.020  1.528
 U52  C4   C5   single    1.520  0.020  1.520
 U52  C4   N2   single    1.336  0.020  1.336
 U52  C28  N20  single    1.450  0.020  1.450
 U52  C30  C31  single    1.528  0.020  1.528
 U52  C18  C17  aromatic  1.384  0.020  1.384
 U52  C18  N19  single    1.400  0.020  1.400
 U52  C1   N2   single    1.445  0.020  1.445
 U52  N20  C32  single    1.449  0.020  1.449
 U52  N20  C24  single    1.352  0.020  1.352
 U52  N23  C24  aromatic  1.336  0.020  1.336
 U52  N23  C22  aromatic  1.319  0.020  1.319
 U52  N19  C22  single    1.353  0.020  1.353
 U52  C31  C32  single    1.527  0.020  1.527
 U52  C31  C34  single    1.522  0.020  1.522
 U52  C24  N25  aromatic  1.339  0.020  1.339
 U52  C22  C27  aromatic  1.410  0.020  1.410
 U52  N25  C26  aromatic  1.324  0.020  1.324
 U52  C27  C26  aromatic  1.374  0.020  1.374
 U52  C27  CL1  single    1.729  0.020  1.729
 U52  C5   H1   single    0.970  0.020  1.090
 U52  C5   H2   single    0.970  0.020  1.090
 U52  C8   H3   single    0.970  0.020  1.090
 U52  C8   H4   single    0.970  0.020  1.090
 U52  C8   H5   single    0.970  0.020  1.090
 U52  C13  H6   single    0.930  0.020  1.080
 U52  C17  H7   single    0.930  0.020  1.080
 U52  C26  H8   single    0.930  0.020  1.080
 U52  C28  H9   single    0.970  0.020  1.090
 U52  C28  H10  single    0.970  0.020  1.090
 U52  C1   H11  single    0.970  0.020  1.090
 U52  C1   H12  single    0.970  0.020  1.090
 U52  C1   H13  single    0.970  0.020  1.090
 U52  N2   H14  single    0.860  0.020  1.020
 U52  C12  H15  single    0.930  0.020  1.080
 U52  C14  H16  single    0.930  0.020  1.080
 U52  N19  H17  single    0.860  0.020  1.020
 U52  C29  H18  single    0.970  0.020  1.090
 U52  C30  H19  single    0.970  0.020  1.090
 U52  C30  H20  single    0.970  0.020  1.090
 U52  C31  H21  single    0.970  0.020  1.090
 U52  C32  H22  single    0.970  0.020  1.090
 U52  C32  H23  single    0.970  0.020  1.090
 U52  C33  H24  single    0.970  0.020  1.090
 U52  C33  H25  single    0.970  0.020  1.090
 U52  C33  H26  single    0.970  0.020  1.090
 U52  C34  H27  single    0.970  0.020  1.090
 U52  C34  H28  single    0.970  0.020  1.090
 U52  C34  H29  single    0.970  0.020  1.090

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 U52  O3   C4   N2   123.87  3.000
 U52  N2   C4   C5   113.99  3.000
 U52  O3   C4   C5   122.09  3.000
 U52  H2   C5   H1   107.41  3.000
 U52  H2   C5   O6   111.30  3.000
 U52  H1   C5   O6   111.07  3.000
 U52  H2   C5   C4   111.32  3.000
 U52  H1   C5   C4   108.16  3.000
 U52  O6   C5   C4   107.57  3.000
 U52  C11  C10  N9   116.08  3.000
 U52  C11  C10  O7   121.13  3.000
 U52  N9   C10  O7   122.79  3.000
 U52  H6   C13  C18  119.74  3.000
 U52  H6   C13  C14  118.98  3.000
 U52  C18  C13  C14  121.27  3.000
 U52  C16  C15  C14  118.62  3.000
 U52  C16  C15  N9   119.58  3.000
 U52  C14  C15  N9   121.80  3.000
 U52  H7   C17  C18  120.71  3.000
 U52  H7   C17  C16  118.52  3.000
 U52  C18  C17  C16  120.77  3.000
 U52  C27  C22  N23  119.79  3.000
 U52  C27  C22  N19  120.71  3.000
 U52  N23  C22  N19  119.50  3.000
 U52  N25  C24  N23  124.81  3.000
 U52  N25  C24  N20  117.94  3.000
 U52  N23  C24  N20  117.24  3.000
 U52  H8   C26  C27  119.74  3.000
 U52  H8   C26  N25  116.85  3.000
 U52  C27  C26  N25  123.41  3.000
 U52  H10  C28  H9   107.60  3.000
 U52  H10  C28  C29  109.48  3.000
 U52  H9   C28  C29  111.12  3.000
 U52  H10  C28  N20  108.07  3.000
 U52  H9   C28  N20  109.66  3.000
 U52  C29  C28  N20  110.80  3.000
 U52  H14  N2   C1   118.13  3.000
 U52  H14  N2   C4   119.51  3.000
 U52  C1   N2   C4   122.37  3.000
 U52  C11  O6   C5   117.39  3.000
 U52  C15  N9   C10  123.52  3.000
 U52  C15  N9   C8   118.43  3.000
 U52  C10  N9   C8   118.05  3.000
 U52  C12  C11  O6   126.80  3.000
 U52  C12  C11  C10  121.63  3.000
 U52  O6   C11  C10  111.57  3.000
 U52  H15  C12  C16  117.85  3.000
 U52  H15  C12  C11  121.97  3.000
 U52  C16  C12  C11  120.18  3.000
 U52  H16  C14  C15  121.39  3.000
 U52  H16  C14  C13  118.17  3.000
 U52  C15  C14  C13  120.44  3.000
 U52  C12  C16  C17  120.69  3.000
 U52  C17  C16  C15  120.30  3.000
 U52  C12  C16  C15  119.00  3.000
 U52  N19  C18  C17  123.52  3.000
 U52  N19  C18  C13  117.81  3.000
 U52  C17  C18  C13  118.59  3.000
 U52  H17  N19  C18  115.52  3.000
 U52  H17  N19  C22  116.43  3.000
 U52  C18  N19  C22  127.78  3.000
 U52  C32  N20  C28  113.26  3.000
 U52  C32  N20  C24  122.06  3.000
 U52  C28  N20  C24  122.19  3.000
 U52  C24  N23  C22  119.10  3.000
 U52  C26  N25  C24  116.09  3.000
 U52  CL1  C27  C26  121.35  3.000
 U52  CL1  C27  C22  121.89  3.000
 U52  C26  C27  C22  116.75  3.000
 U52  H18  C29  C33  108.57  3.000
 U52  H18  C29  C30  108.74  3.000
 U52  C33  C29  C30  111.51  3.000
 U52  H18  C29  C28  107.52  3.000
 U52  C30  C29  C28  109.94  3.000
 U52  C33  C29  C28  110.46  3.000
 U52  H20  C30  H19  106.28  3.000
 U52  H20  C30  C31  108.33  3.000
 U52  H19  C30  C31  110.00  3.000
 U52  H20  C30  C29  108.67  3.000
 U52  H19  C30  C29  109.98  3.000
 U52  C31  C30  C29  113.31  3.000
 U52  H21  C31  C34  108.69  3.000
 U52  H21  C31  C32  107.66  3.000
 U52  C34  C31  C32  110.46  3.000
 U52  H21  C31  C30  108.90  3.000
 U52  C34  C31  C30  111.43  3.000
 U52  C32  C31  C30  109.61  3.000
 U52  H23  C32  H22  107.58  3.000
 U52  H23  C32  C31  111.16  3.000
 U52  H22  C32  C31  109.30  3.000
 U52  H23  C32  N20  109.73  3.000
 U52  H22  C32  N20  107.81  3.000
 U52  C31  C32  N20  111.13  3.000
 U52  H26  C33  H25  107.64  3.000
 U52  H26  C33  H24  107.78  3.000
 U52  H25  C33  H24  107.63  3.000
 U52  H26  C33  C29  111.49  3.000
 U52  H25  C33  C29  111.20  3.000
 U52  H24  C33  C29  110.93  3.000
 U52  H29  C34  H28  107.97  3.000
 U52  H29  C34  H27  107.71  3.000
 U52  H28  C34  H27  107.24  3.000
 U52  H29  C34  C31  111.28  3.000
 U52  H28  C34  C31  111.39  3.000
 U52  H27  C34  C31  111.05  3.000
 U52  H5   C8   H4   109.05  3.000
 U52  H5   C8   H3   108.68  3.000
 U52  H4   C8   H3   108.65  3.000
 U52  H5   C8   N9   110.59  3.000
 U52  H4   C8   N9   110.36  3.000
 U52  H3   C8   N9   109.47  3.000
 U52  H13  C1   H12  108.41  3.000
 U52  H13  C1   H11  108.42  3.000
 U52  H12  C1   H11  108.41  3.000
 U52  H13  C1   N2   111.43  3.000
 U52  H12  C1   N2   108.35  3.000
 U52  H11  C1   N2   111.72  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 U52  CONST_01  C16  C15  C14  C13     0.00   0.0  0
 U52  CONST_02  C16  C17  C18  C13     0.00   0.0  0
 U52  CONST_03  C18  C13  C14  C15     0.00   0.0  0
 U52  CONST_04  C18  C17  C16  C15     0.00   0.0  0
 U52  CONST_05  C14  C15  C16  C17     0.00   0.0  0
 U52  CONST_06  C14  C13  C18  C17     0.00   0.0  0
 U52  CONST_07  N25  C24  N23  C22     0.00   0.0  0
 U52  CONST_08  N25  C26  C27  C22     0.00   0.0  0
 U52  CONST_09  C27  C22  N23  C24     0.00   0.0  0
 U52  CONST_10  C27  C26  N25  C24     0.00   0.0  0
 U52  CONST_11  N23  C24  N25  C26     0.00   0.0  0
 U52  CONST_12  N23  C22  C27  C26     0.00   0.0  0
 U52  CONST_13  N20  C24  N23  C22   180.00   0.0  0
 U52  CONST_14  N20  C24  N25  C26   180.00   0.0  0
 U52  CONST_15  C11  C10  N9   C15     0.00   0.0  0
 U52  CONST_16  N19  C22  N23  C24   180.00   0.0  0
 U52  CONST_17  N19  C22  C27  C26   180.00   0.0  0
 U52  CONST_18  N19  C18  C13  C14   180.00   0.0  0
 U52  CONST_19  N19  C18  C17  C16   180.00   0.0  0
 U52  CONST_20  N23  C22  C27  CL1   180.00   0.0  0
 U52  CONST_21  N25  C26  C27  CL1   180.00   0.0  0
 U52  CONST_22  C11  C10  N9   C8    180.00   0.0  0
 U52  CONST_23  O7   C10  N9   C15   180.00   0.0  0
 U52  CONST_24  H7   C17  C18  C13   180.00   0.0  0
 U52  CONST_25  H6   C13  C14  C15   180.00   0.0  0
 U52  CONST_26  H8   C26  C27  C22   180.00   0.0  0
 U52  CONST_27  H16  C14  C15  N9      0.00   0.0  0
 U52  CONST_28  O7   C10  N9   C8      0.00   0.0  0
 U52  CONST_29  C1   N2   C4   C5    180.00   0.0  0
 U52  CONST_30  O3   C4   N2   C1      0.00   0.0  0
 U52  CONST_31  H14  N2   C4   C5      0.00   0.0  0
 U52  Var_01    C29  C28  N20  C24  -102.41  30.0  1
 U52  Var_02    C31  C32  N20  C24   102.09  30.0  1
 U52  Var_03    N23  C24  N20  C28   167.23  30.0  2
 U52  Var_04    C22  N19  C18  C13   146.89  30.0  2
 U52  Var_05    N23  C22  N19  C18    -3.65  30.0  2
 U52  Var_06    C10  C11  O6   C5    179.94  30.0  2
 U52  Var_07    H3   C8   N9   C10     2.98  30.0  3
 U52  Var_08    H1   C5   O6   C11    58.80  30.0  3
 U52  Var_09    O6   C5   C4   N2    156.38  30.0  3
 U52  Var_10    H11  C1   N2   C4     64.96  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 U52  chir_01  C29  C33  C28  C30  positiv
 U52  chir_02  C31  C30  C32  C34  positiv

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 U52  plan-1  C22  0.020
 U52  plan-1  C24  0.020
 U52  plan-1  C26  0.020
 U52  plan-1  N19  0.020
 U52  plan-1  N20  0.020
 U52  plan-1  N23  0.020
 U52  plan-1  N25  0.020
 U52  plan-1  C27  0.020
 U52  plan-1  H8   0.020
 U52  plan-1  CL1  0.020
 U52  plan-2  C10  0.020
 U52  plan-2  C13  0.020
 U52  plan-2  C15  0.020
 U52  plan-2  C17  0.020
 U52  plan-2  O6   0.020
 U52  plan-2  O7   0.020
 U52  plan-2  N9   0.020
 U52  plan-2  C11  0.020
 U52  plan-2  C12  0.020
 U52  plan-2  C14  0.020
 U52  plan-2  C16  0.020
 U52  plan-2  C18  0.020
 U52  plan-2  N19  0.020
 U52  plan-2  H6   0.020
 U52  plan-2  H7   0.020
 U52  plan-2  H15  0.020
 U52  plan-2  H16  0.020
 U52  plan-2  C8   0.020
 U52  plan-3  C4   0.020
 U52  plan-3  C5   0.020
 U52  plan-3  N2   0.020
 U52  plan-3  O3   0.020
 U52  plan-3  H14  0.020
 U52  plan-3  C1   0.020

